6LNP

Crystal structure of citrate Biosensor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

High-Performance Intensiometric Direct- and Inverse-Response Genetically Encoded Biosensors for Citrate.

Zhao, Y.Shen, Y.Wen, Y.Campbell, R.E.

(2020) ACS Cent Sci 6: 1441-1450

  • DOI: https://doi.org/10.1021/acscentsci.0c00518
  • Primary Citation of Related Structures:  
    6LNP

  • PubMed Abstract: 

    Motivated by the growing recognition of citrate as a central metabolite in a variety of biological processes associated with healthy and diseased cellular states, we have developed a series of high-performance genetically encoded citrate biosensors suitable for imaging of citrate concentrations in mammalian cells. The design of these biosensors was guided by structural studies of the citrate-responsive sensor histidine kinase and took advantage of the same conformational changes proposed to propagate from the binding domain to the catalytic domain. Following extensive engineering based on a combination of structure guided mutagenesis and directed evolution, we produced an inverse-response biosensor (Δ F / F min ≈ 18) designated Citroff1 and a direct-response biosensor (Δ F / F min ≈ 9) designated Citron1. We report the X-ray crystal structure of Citron1 and demonstrate the utility of both biosensors for qualitative and quantitative imaging of steady-state and pharmacologically perturbed citrate concentrations in live cells.


  • Organizational Affiliation

    Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of Green fluorescent protein and Sensor histidine kinase CitAA [auth B],
B [auth D]
403Aequorea victoriaKlebsiella pneumoniaeMutation(s): 0 
EC: 2.7.13.3
UniProt
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P52687 (Klebsiella pneumoniae)
Explore P52687 
Go to UniProtKB:  P52687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P52687
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
A [auth B],
B [auth D]
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.229 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.41α = 90
b = 92.41β = 90
c = 123.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870132

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description